Viruses and CRISPR · What you can do here
Find CRISPR arrays and Cas genes in a genome
Identify CRISPR arrays, predict Cas operons, and classify subtypes across bacterial, archaeal, or metagenomic assemblies without local software installation.
What this involves
A CRISPR array acts as a genomic record of past infections, comprising direct repeats separated by variable spacers acquired from mobile genetic elements. Detecting these loci together with their associated Cas genes provides insight into an organism's adaptive immune capacity and functional subtypes. However, simple pattern matching frequently misidentifies tandem repeats as arrays or fails to orient the locus correctly.
Analyzing CRISPR-Cas loci properly requires distinguishing true biological systems from low-complexity repeat sequences, resolving locus orientation to determine the leader end containing the newest spacers, and typing the Cas operon. Approximately half of bacteria and most archaea harbor CRISPR-Cas systems; an absence of detected systems is an informative result, but it depends strictly on assembly completeness and detection thresholds.
The research agent carries out this analysis directly on an isolated execution environment using MinCED and CRISPRCasFinder. It ingests NCBI accessions, uploaded FASTA sequences, or remote URLs, caches the sequence files locally, runs the detection software, and returns typed arrays, spacer profiles, and Cas gene coordinates.
How it goes
- 1Sequence ingestion and stagingThe agent loads an NCBI nucleotide accession, a path from the workspace upload directory, or a FASTA URL, downloading assembly fastas via the NCBI datasets CLI when given GCF accessions.
- 2Rapid array screeningMinCED scans contigs to rapidly identify CRISPR repeat-spacer architectures, capturing array boundaries and spacer sequences across fragmented or metagenomic assemblies.
- 3Cas typing and evidence scoringCRISPRCasFinder evaluates candidate loci to assign evidence levels from 1 to 4, determine array orientation, and type Cas clusters using MacSyFinder and CasFinder according to the Makarova classification.
- 4Spacer target investigationExtracted spacer sequences are aligned against viral or plasmid nucleotide sets using blastn with short-query parameters (-task blastn-short, -word_size 7, -evalue 1e-3) to identify protospacer targets.
Start it here
Ask in plain language. The agent works on a Linux machine of its own — it installs and runs what the job needs, keeps every file, and reads the results back with the numbers explained. Nothing to set up, and a long run continues after you close the page.
What to watch for
- Arrays graded at evidence level 1 or 2 in CRISPRCasFinder are tandem repeats or short candidates and should not be reported as true CRISPR arrays.
- MinCED does not determine array orientation, meaning the most recently acquired spacer at the leader end cannot be inferred from its output alone.
- A repeat count of two is not an intact array; MinCED can be configured to detect two repeats on short metagenomic contigs, but these must be reported strictly as fragments.
- Tandem repeats and low-complexity regions mimic arrays, but can be distinguished because their spacer units resemble one another or the repeat itself.
- Identical repeat consensus sequences split across multiple contigs belong to the same array and must be merged rather than counted separately.
- Searching for Cas genes on short, unbinned metagenomic contigs yields no usable detections because operons span several kilobases.
What it runs
Questions
Do I need to install anything to find crispr arrays and cas genes in a genome?
No. The research agent does this work on a Linux machine of its own — it runs MinCED, CRISPRCasFinder there, keeps the files, and reads the results back to you. Long runs continue if you close the page.
When should MinCED be used instead of CRISPRCasFinder?
MinCED is fast and well suited for screening large numbers of metagenomic contigs where only array architecture is needed. CRISPRCasFinder is preferred for complete genomes or long contigs where Cas gene typing, evidence levels, and locus orientation are required.
What do the CRISPRCasFinder evidence levels mean?
Levels 3 and 4 indicate reliable or confident arrays characterized by conserved repeats and distinct spacers. Levels 1 and 2 indicate short candidates or tandem repeats that should be excluded from final reports.
Can CRISPR-Cas systems be detected directly from raw metagenomic reads?
No. Detection tools require assembled contigs or binned sequences rather than raw sequencing reads to locate repeat-spacer patterns and Cas operons.
How are Cas genes classified by the platform?
CRISPRCasFinder uses MacSyFinder and CasFinder to classify Cas clusters into Class 1 (multi-subunit effectors: types I, III, IV) or Class 2 (single effectors: types II, V, VI) and names the exact subtype, such as I-E or II-A.
Written from the method the research agent follows for this work and the documentation of the tools listed above. Statements citing a figure that does not appear there are removed before publication. Corollary is a non-commercial research demonstration; results are not for clinical use.